ProLint v2: an optimized tool for the analysis of lipid protein interactions.

Overview

ProLint2 calculates distance-based lipid-protein interactions from molecular dynamics trajectories of membrane protein systems.

Table of contents

• Installation
• Basic examples
• How to contribute?
• License
• Copyright
• Acknowledgements

Installation

To install prolint2 we recommend creating a new conda environment as follows:

   conda create -n prolint2 python=3.8
   conda activate prolint2

Then you can install prolint2 via pip:

   pip install prolint2

Basic examples:

Using the Prolint2's API:

   from prolint2 import Universe
   from prolint2.sampledata import GIRKDataSample
   GIRK = GIRKDataSample()

   u = Universe(GIRK.coordinates, GIRK.trajectory)

   contacts = u.compute_contacts(cutoff=7) # cutoff in Angstroms

Using the Prolint2's command-line interface:

   prolint2 coordinates.gro trajectory.xtc -c 7

You can find more details on how to use prolint2 in the documentation.

How to contribute?

If you find a bug in the source code, you can help us by submitting an issue here. Even better, you can submit a Pull Request with a fix.

We really appreciate your feedback!

License

Source code included in this project is available under the MIT License.

Copyright

Copyright (c) 2022, Daniel P. Ramirez & Besian I. Sejdiu

Acknowledgements

The respository structure of ProLint2 is based on the Computational Molecular Science Python Cookiecutter version 1.6.